[MOBY-l] moby-l at biomoby.org

[Vijay Narayanasamy]

Thank you Ken, The problem was caused by printing from the Java code
(System.out.println()). I use Perl Inline Java module to wrap the Java
Pubfetch program for Agricola.

The PubFetch service for Agricola works OK now at my local BioMOBY. I will
register the service with public BioMOBY soon.

Thank you,

Vijay

-----Original Message-----
From: Ken Steube [mailto:steube at sdsc.edu] 
Sent: Monday, February 02, 2004 3:22 PM
To: Vijay Narayanasamy
Cc: 'Mark Wilkinson'; Twigger, Simon; 'moby-l at biomoby.org'
Subject: Re: [MOBY-l] moby-l at biomoby.org

Mark may still be preoccupied with moving so I'll take a crack at this.

> But the MOBY client (Old Client) reports "service unavailable"

You can't always debug a service thru the client...you don't get any error
messages. Here's a summary of what I usually do when in your situation:

There are several reasons services fail and you have to do some
experiments to figure it out:

1) Maybe the CGI is not being called.  Go to the top of your dispatcher
CGI (the one you give when you register the service) and before the
dispatch_with() call add this:

  die "testing xxxxxx";

If you see xxxxxx in your http error log you know it's getting to this
CGI.

2) Maybe it's not dispatching. Go to the top of the method for your
service (sub has the same name as the service) and add a line at the top

  return("testing yyyyyy");

Run the service from a script at the command line and see if you get this
yyyyyy line returned from the service. Once you get it you know the
service is being called.

3) Maybe your service has a compile-time error and the error message
doesn't wind up in the http error log for some reason. Run a script like
the attached to execute your service at the command line. The attached
script runs the method of a service by calling it as a subroutine with no
SOAP involvement. Look for compiler errors.

Ken




On Mon, 2 Feb 2004, Vijay Narayanasamy wrote:

> Hi Mark,
>
> I am currently developing a PubFetch Service for Agricola literature
> database similar to PubFetch service for PubMed.
>
> I have two services. Both use namespace "Global_Keyword" for inputs and
> outputs and the object is "Object" (I'll change the namespace and object
> type once I get it working)
>
> One service takes the query and retrieves the Agricola accession numbers.
> This works OK!
>
>
> The second service takes the Agricola accession numbers as input and gets
> the document in Medline Like format as shown in the following MOBY
response
>
> <?xml version='1.0' encoding='UTF-8'?>
>       <moby:MOBY xmlns:moby='http://www.biomoby.org/moby'>
>         <moby:Response moby:authority='http://www.illuminae.com'>
>
>         <moby:queryResponse>
>             <Simple><moby:Object namespace='Global_Keyword'
> id='IND23321742'><![CDATA[
> AN -   IND23321742
> XX -   3321-74260
> OWN -   AGL
> XX -   F600
> XX -   F200
> AU -   Lee, G.I.
> TI -   1H, 13C and 15N resonance assignments of the kinase-interacting FHA
> domain of Arabidopsis thaliana kinase-associated protein phosphatase.
> PG -   p. 253-254.
> GN -   Letter to the editor.
> XX -   Includes references
> OT -   spectral analysis
> OT -   nuclear magnetic resonance spectroscopy
> OT -   amino acid sequences  Internet-resource.
> AU -   Li, J.
> AU -   Walker, J.C.
> AU -   Van Doren, S.R.
> SO -   Journal of biomolecular NMR.  J. biomol. NMR  Mar 2003. v. 25 (3)
> 0925-2738  JBNME9  nnas  jnl52412
> XX -   0667-68060
> CA -     QP519.9.N83 J68
> http://www.kluweronline.com/issn/0925-2738/contents
> XX -   20030508  20030509  00000000  IND  GK1
> Non-US]]></moby:Object></Simple>
>         </moby:queryResponse>
>
>     </moby:Response>
>       </moby:MOBY>
>
>
> But the MOBY client (Old Client) reports "service unavailable" for this
> service. I don't see any error message in the apache log files. What could
> be a possible reason?
>
> Thank you,
>
> Vijay
>
>
>
> Vijay Narayanasamy
> Project Programmer / Analyst
> Bioinformatics Program, Human and Molecular Genetics Center
> Medical College of Wisconsin
> 8701, W. Watertown Plank Road
> Milwaukee, WI 53226
> 414-456-8026
> vnarayan at mcw.edu
> http://brc.mcw.edu/
>
>
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>

-- 
--
--
Ken Steube
San Diego Supercomputer Center
University of California, San Diego, MC 0505
9500 Gilman Drive
San Diego, California, 92093-0505  USA
FAX (858) 822-3610